read.bed: Reading data from binary PLINK files

Description Usage Arguments Value Examples

View source: R/read.bed.R

Description

Loads genotype data from PLINK format files .bed, .bim, and .fam.

Usage

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read.bed(bed, bim, fam, sel.snps = NULL, sel.subs = NULL, encode012 = TRUE)

Arguments

bed

the name of the bed file.

bim

the name of the bim file. For a SNP without a rs number, use any character (including any white space or '.') in the second column of the bim file.

fam

the name of the fam file.

sel.snps

a character vector of SNPs to be extracted from the plink files. The default is NULL, i.e., all SNPs are extracted. SNPs could be named by its rs number (e.g. rs1234), or by Chr:Pos (e.g. 13:234567, or C13P234567) if a rs number is not available. All other naming methods for a SNP are not accepted in current version.

sel.subs

an optional character vector specifying a subset of subject IDs to be extracted from the plink files. These IDs should be matched with the second column of fam files. The default is NULL, i.e., all subjects are extracted.

encode012

logical. Encoding the genotypes using 0/1/2 if TRUE, or using symbols of the reference and effect alleles if FALSE. The default is TRUE.

Value

A data frame of genotypes of specified subjects in the plink files. For a SNP in sel.snps specified in the format Chr:Pos, e.g. 13:234567, it will be named to be C13P234567 in the returned data frame.

Examples

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# Load the sample data

bed <- system.file("extdata", package = 'ARTP2', 'chr1.bed')
bim <- system.file("extdata", package = 'ARTP2', 'chr1.bim')
fam <- system.file("extdata", package = 'ARTP2', 'chr1.fam')

## first five SNPs
b <- read.table(bim, header = FALSE, as.is = TRUE, nrows = 5)
## first 50 subjects
f <- read.table(fam, header = FALSE, as.is = TRUE, nrows = 50)
geno <- read.bed(bed, bim, fam, sel.snps = b[, 2], sel.subs = f[, 2])

dim(geno) # 50 x 5

ARTP2 documentation built on Dec. 1, 2018, 1:05 a.m.